I also freeze mine whole, for the same reason P. Dreadie gave... as a "unit" of measurement. Pluck off the plant, rinse in warm water, let sit on wax paper to air dry (a fan helps). Then use paper towels to wipe any excess water (if any), drop in freezer bags, and put 'em away.
I noticed some of my habaneros from different times of the growing season had different heat levels... this method will also allow you to keep track of that if you use multiple freezer bags. And those tiny habs last year... they always seemed to be weaker. If they were all chopped up, I'd never know, and I'd have a hell of a time finding out how many pieces are "three habaneros."